From: peterjc
Date: Thu, 22 Mar 2012 17:49:40 +0000 (+0000)
Subject: Check current reference sequence matches RNAME in samtools depad
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=70c84f409b060067e70087e51b29700215cbddbb;p=samtools.git
Check current reference sequence matches RNAME in samtools depad
---
diff --git a/padding.c b/padding.c
index 4290485..ad68728 100644
--- a/padding.c
+++ b/padding.c
@@ -45,7 +45,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
} else if (op == BAM_CDEL) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
} else {
- fprintf(stderr, "[unpad_seq] Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
assert(-1);
}
}
@@ -56,6 +56,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
bam_header_t *h;
bam1_t *b;
kstring_t r, q;
+ int r_tid = -1;
uint32_t *cigar2 = 0;
int n2 = 0, m2 = 0, *posmap = 0;
@@ -68,6 +69,10 @@ int bam_pad2unpad(bamFile in, bamFile out)
n2 = 0;
if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
int i, k;
+ /*
+ fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+ */
+ r_tid = b->core.tid;
unpad_seq(b, &r);
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
@@ -76,8 +81,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
posmap[i] = k; // note that a read should NOT start at a padding
if (r.s[i]) ++k;
}
- } else {
+ } else if (b->core.n_cigar > 0) {
int i, k, op;
+ if (b->core.tid < 0) {
+ fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
+ return -1;
+ } else if (b->core.tid != r_tid) {
+ fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
+ return -1;
+ }
unpad_seq(b, &q);
if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
@@ -110,13 +122,14 @@ int bam_pad2unpad(bamFile in, bamFile out)
int main_pad2unpad(int argc, char *argv[])
{
bamFile in, out;
+ int result=0;
if (argc == 1) {
fprintf(stderr, "Usage: samtools depad \n");
return 1;
}
in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
out = bam_dopen(fileno(stdout), "w");
- bam_pad2unpad(in, out);
+ result = bam_pad2unpad(in, out);
bam_close(in); bam_close(out);
- return 0;
+ return result;
}